Literature DB >> 11027326

Catalytic tempering: A method for sampling rough energy landscapes by Monte Carlo.

G Stolovitzky1, B J Berne.   

Abstract

A new Monte Carlo algorithm is presented for the efficient sampling of the Boltzmann distribution of configurations of systems with rough energy landscapes. The method is based on the introduction of a fictitious coordinate y so that the dimensionality of the system is increased by one. This augmented system has a potential surface and a temperature that is made to depend on the new coordinate y in such a way that for a small strip of the y space, called the "normal region," the temperature is set equal to the temperature desired and the potential is the original rough energy potential. To enhance barrier crossing outside the "normal region," the energy barriers are reduced by truncation (with preservation of the potential minima) and the temperature is made to increase with ||y ||. The method, called catalytic tempering or CAT, is found to greatly improve the rate of convergence of Monte Carlo sampling in model systems and to eliminate the quasi-ergodic behavior often found in the sampling of rough energy landscapes.

Entities:  

Year:  2000        PMID: 11027326      PMCID: PMC17171          DOI: 10.1073/pnas.97.21.11164

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  4 in total

1.  Nonuniversal critical dynamics in Monte Carlo simulations.

Authors: 
Journal:  Phys Rev Lett       Date:  1987-01-12       Impact factor: 9.161

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Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1994-11

Review 3.  Novel methods of sampling phase space in the simulation of biological systems.

Authors:  B J Berne; J E Straub
Journal:  Curr Opin Struct Biol       Date:  1997-04       Impact factor: 6.809

4.  Monte Carlo-minimization approach to the multiple-minima problem in protein folding.

Authors:  Z Li; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1987-10       Impact factor: 11.205

  4 in total
  2 in total

1.  Replica exchange with solute tempering: a method for sampling biological systems in explicit water.

Authors:  Pu Liu; Byungchan Kim; Richard A Friesner; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-19       Impact factor: 11.205

2.  Error and efficiency of simulated tempering simulations.

Authors:  Edina Rosta; Gerhard Hummer
Journal:  J Chem Phys       Date:  2010-01-21       Impact factor: 3.488

  2 in total

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